Asst.-Prof. Dr. Dagmar Woebken

The overarching goal of my research group is to better understand the active microbial participants in key processes within the terrestrial carbon (C)- and nitrogen (N) -cycle, the factors that govern these activities, the trophic interactions among microorganisms, but also between plants and microorganisms within an ecosystem, and the physiologies that allow for the success of soil microorganisms. Furthermore, my research group strives to integrate the concepts of ecological theory into the realm of microbial ecology to address fundamental questions about niche differentiation, dormancy and microbial seed bank for processes in the soil C- and N- cycles. In many projects, we are including single-cell methods such as fluorescence in situ hybridization (FISH), high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy to answer our research questions.

Diazotrophy. One of my major research interests explores the diversity of free-living diazotrophs in temperate grasslands and deserts, as free-living diazotrophs may provide more fixed N in these ecosystems than symbiotic diazotrophs. We are using the multidisciplinary approach that was used previously to identify the active diazotroph microbial community members in photosynthetic microbial mats (Woebken et al., 2012 and Woebken et al., 2015). More specifically, we are investigating the diversity of free-living diazotrophs in grassland soil and the dependence of their activity on external factors such as available C sources (e.g. simple sugars in form of root exudates), since N2 fixation is a highly energy demanding process. As a second focus, we are investigating diazotrophy in biological soil crusts, which contribute to ~30% of the total biological N2 fixation in terrestrial ecosystems.

Plant microbiome. Plants and soil microorganisms are major drivers in the terrestrial C- and N- cycles and live in tight associations. The plant-associated microbial community is oftentimes referred to as the ‘plant microbiome’, which is defined as the microorganisms in close proximity or associated with (1) the aerial part of the plant, such as the leaves and stem; and (2) below-ground parts of the plant such as root, the root surface (rhizoplane) and the soil surrounding the roots (rhizosphere).

Soils are believed to be the microbial seed bank or reservoir for this microbiome, from which the plant recruits its associated microbiome by exuding up to 40% of its fixed C into the surrounding soil. With these exudates, a tremendous amount of chemical communication occurs between the plant and microorganisms in this dynamic system and is believed to promote beneficial interactions. As plants can influence microbial N-cycle processes and supply microorganisms with C sources via root exudates, we have extended our diazotrophy investigations into the ‘plant microbiome’ that inhabit the rhizosphere, the rhizoplane or the endosphere compartment of plants. Our model systems include meadow grass plants in Austrian grasslands and rice plants, one of the most important agricultural plant worldwide.

Microbial cellulose degradation. In addition to the N-cycle, we are currently investigating the active participants as well as edaphic drivers and limitations of microbial cellulose degradation. Soils contain the largest pool of C on Earth with cellulose being the most abundant polymer, as it is a key component of plant structural C. Members of the Bacteria and Fungi are responsible for degrading cellulose, but their contributions remain unresolved. For a better understanding of the terrestrial C-cycle it is vital to elucidate the active participants in cellulose degradation and identify different niches of cellulose-responsive guilds. We are combing stable isotope probing with next generation sequencing to characterize cellulose-responsive guilds across various amendments, along with single-cell based approaches to appreciate this process at a more relevant spatial scale.

Acidobacteria. Pick up any handful of soil worldwide, and members of the phylum Acidobacteria will probably be one of the most dominant groups. They comprise a monophyletic phylum of astonishing diversity similar to the proteobacteria, with 26 currently recognized subdivisions. Their prevalence suggests that they play ecologically significant roles in the soil environment, yet we still know very little about (i) the genes/functions, which allow them to be prevalent and (ii) the physiological traits that are important to terrestrial biogeochemical cycles.

Our overarching goal is to better link the genetic potential of acidobacteria with their in situ functions in soil in order to elucidate the ecophysiology and therefore the success and ubiquity of members of the phylum Acidobacteria in terrestrial ecosystems. For this, we combine genomic, growth-based, molecular and single-cell functional analyses. In addition, we are also attempting to cultivate additional strains in this diverse phylum, which is highly unrepresented in culture collections and databases.

Microbial dormancy.Soils are considered the last scientific frontiers that harbor one of the most diverse microbial communities on Earth. It is hypothesized that this diversity allows for redundancy in microbial key processes, thereby ensuring ecosystem stability. Much of this functional redundancy is embodied in non-active, dormant microorganisms that represent the ‘microbial seed bank’. It is hypothesized that dormant microorganisms can be recruited to participate in a given function upon resuscitation with environmental cue(s). We are addressing fundamental questions about functional redundancy, dormancy and the ‘microbial seed bank’ that could explain the extensive diversity of soil microbial communities. The goals of this project are to reveal environmental cues that resuscitate dormant microorganisms involved in major soil functions and to identify the activated microorganisms using an arid ecosystem as a model system and by combining stable isotope probing (SIP) and sequencing with process-level and single-cell activity analysis.

Method development. Across many of these aforementioned projects, we are constantly developing, testing and optimizing single-cell methods to facilitate their application to microorganisms in terrestrial habitats. Single-cell based approaches such as high-resolution secondary ion mass spectrometry (NanoSIMS) and Raman microspectroscopy are increasingly applied in microbial ecology studies. Raman microspectroscopy and NanoSIMS are techniques that permit the analysis of microbiological samples down to the single-cell level. These powerful techniques have recently helped define the field of single-cell ecophysiology especially when combined with stable isotope tracers (such as 13C, 15N and D) and/or identification of the targeted cell using fluorescence in situ hybridization (FISH).

The Woebken GROUP

Joining the team

Information on open research positions can be found here or can be obtained by contacting Dagmar. If you are interested in joining our team with your own fellowship, please check out our PhD & postdoc program.

PhD students in the Woebken group (Florian Strasser and Maximillian Nepel) provided hands-on training in various fluorescence in situ hybridization (FISH) techniques, while Stephanie A. Eichorst and Dagmar Woebken gave webinars on the theory and principle of FISH.

PUBLIC OUTREACH

Summer Workshop entitled "What would the world look like without microbes?". Course description: Microbes are all around us and are very important. Imagine what the world would look like without them? Come spend some time at our Microbe Exhibition and learn more. We will explore what microbes do in nature, for instance in dirt and in lakes, how they help us make food, and how they help plants to grow.

3-day workshop for school children entitled "An Underground Adventure. Dirt - The Scoop on Soil". This 3-day workshop was a synthesis of presentations, discussions and hand-on activities designed to develop an awareness and appreciation for soil and soil microorganisms. The themes covered topics such as "What is Soil?", "What lives in soil?", and what we can do to save/preserve the soil, jobs with soil and a question-and-answer session with the students.